Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray

We have performed microarray hybridization studies on 40 clinical isolates from 12 common serovars within Salmonella enterica subspecies I to identify the conserved chromosomal gene pool. We were able to separate the core invariant portion of the genome by a novel mathematical approach using a decision tree based on genes ranked by increasing variance. All genes within the core component were confirmed using available sequence and microarray information for S. enterica subspecies I strains. The majority of genes within the core component had conserved homologues in Escherichia coli K-12 strain MG1655. However, many genes present in the conserved set which were absent or highly divergent in K-12 had close homologues in pathogenic bacteria such as Shigella flexneri and Pseudomonas aeruginosa. Genes within previously established virulence determinants such as SPI1 to SPI5 were conserved. In addition several genes within SPI6, all of SPI9, and three fimbrial operons (fim, bcf, and stb) were conserved within all S. enterica strains included in this study. Although many phage and insertion sequence elements were missing from the core component, approximately half the pseudogenes present in S. enterica serovar Typhi were conserved. Furthermore, approximately half the genes conserved in the core set encoded hypothetical proteins. Separation of the core and variant gene sets within S. enterica subspecies I has offered fundamental biological insight into the genetic basis of phenotypic similarity and diversity across S. enterica subspecies I and shown how the core genome of these pathogens differs from the closely related E. coli K-12 laboratory strain.

Nitrogen speciation and phosphorus fractionation dynamics in a lowland chalk catchment

A detailed analysis of temporal and spatial trends in nitrogen (N) speciation and phosphorus (P) fractionation in the Wylye, a lowland Chalk sub-catchment of the Hampshire Avon, UK is presented, identifying the sources contributing to nutrient enrichment, and temporal variability in the fractionation of nutrients in transit from headwaters to lower reaches of the river. Samples were collected weekly from ten monitoring stations with daily sampling at three further sites over one year, and monthly inorganic N and total reactive P (TRP) concentrations at three of the ten weekly monitoring stations over a ten year period are also presented. The data indicate significant daily and seasonal variation in nutrient fractionation in the water column, resulting from plant uptake of dissolved organic and inorganic nutrient fractions in the summer months, increased delivery of both N and P from diffuse sources in the autumn to winter period and during high flow events, and lack of dilution of point source discharges to the Wylye from septic tank, small package Sewage Treatment Works (STW) and urban Waste Water Treatment Works (WwTW) during the summer low flow period. Weekly data show that contributing source areas vary along the river with headwater N and P strongly influenced by diffuse inorganic N and particulate P fluxes, and SRP and organic-rich point source contributions from STW and WwTW having a greater influence in the lower reaches. Long-term data show a decrease in TRP concentrations at all three monitoring stations, with the most pronounced decrease occurring downstream from Warminster WwTW, following the introduction of P stripping at the works in 2001. Inorganic N demonstrates no statistically significant change over the ten year period of record in the rural headwaters, but an increase in the lower reaches downstream from the WwTW which may be due to urban expansion in the lower catchment.

Investigation of sainfoin (Onobrychis viciifolia) cultivar differences on nitrogen balance and fecal egg count in artificially infected lambs

Research in ruminant nutrition and helminth control with forages, which contain condensed tannins (CT), suggests that varying responses may depend not only on CT concentration but also on CT composition. An experiment was designed to test this by feeding 2 dried sainfoin cultivars (Visnovsky and Perly), which differed in CT properties, to lambs that were artificially infected with the abomasal blood-sucking nematode Haemonchus contortus. Twenty-four infected lambs received one of these 2 cultivars; the feeds were either untreated or treated with the CT-binding polyethylene glycol over 4 wk (n = 6). The 2 cultivars were also fed to 2 × 6 uninfected lambs. Nutrient digestibility, N balance, ADG, plasma urea together with indicators of infection [fecal egg count (FEC), abomasal worm count, per capita female fecundity, erythrocytic indices, and serum protein] were determined. The specific effects of sainfoin cultivar, CT, and infection were evaluated by contrast analysis. Digestibility of both NDF and ADF were lower (P < 0.001) with Perly compared to Visnovsky. The apparent nutrient digestibility was reduced (P < 0.001) by CT. However, no clear cultivar effects were evident on N excretion and retention. Condensed tannins reduced (P = 0.05) body N retention and shifted (P < 0.001) N excretion from urine to feces. Unlike cultivar and CT, infection decreased (P = 0.002) ADG. Plasma urea concentration was lower (P = 0.007) in Perly- compared to Visnovsky-fed lambs and was decreased (P < 0.001) by CT. Plasma concentrations of essential and semi-essential AA were increased (P < 0.001) by CT. The groups of infected lambs did not clearly differ in abomasal worm counts and erythrocytic indicators. In the last 2 to 3 wk of the experiment, FEC was lower (P ≤ 0.01) when feeding CT. The lack of substantial cultivar effects suggests that the differences in CT properties may have been too small to result in nutritional and anthelmintic effects. The present results indicate that sainfoin CT had a mitigating effect on FEC and, consequently, pasture infectivity. However, the reduction was too low to expect any significant benefits in an Haemonchus-dominated system. Therefore, the use of sainfoin for controlling H. contortus should only be one component within an integrated worm control system.

Credit and liquidity components of corporate CDS spreads

This paper investigates the role of credit and liquidity factors in explaining corporate CDS price changes during normal and crisis periods. We find that liquidity risk is more important than firm-specific credit risk regardless of market conditions. Moreover, in the period prior to the recent “Great Recession” credit risk plays no role in explaining CDS price changes. The dominance of liquidity effects casts serious doubts on the relevance of CDS price changes as an indicator of default risk dynamics. Our results show how multiple liquidity factors including firm specific and aggregate liquidity proxies as well as an asymmetric information measure are critical determinants of CDS price variations. In particular, the impact of informed traders on the CDS price increases when markets are characterised by higher uncertainty, which supports concerns of insider trading during the crisis.

Enantiomeric conformation controls rate and yield of photoinduced electron transfer in DNA sensitized by Ru(II) Dipyridophenazine complexes

Photosensitized oxidation of guanine is an important route to DNA damage. Ruthenium polypyridyls are very useful photosensitizers as their reactivity and DNA-binding properties are readily tunable. Here we show a strong difference in the reactivity of the two enantiomers of [Ru(TAP)2(dppz)]2+, by using time-resolved visible and IR spectroscopy. This reveals that the photosensitized one-electron oxidation of guanine in three oligonucleotide sequences proceeds with similar rates and yields for bound delta-[Ru(TAP)2(dppz)]2+, whereas those for the lambda enantiomer are very sensitive to base sequence. It is proposed that these differences are due to preferences of each enantiomer for different binding sites in the duplex.

The effects of tannin-containing ground pine bark diet upon nutrient digestion, nitrogen balance, and mineral retention in meat goats

Background Pine bark is a rich source of phytochemical compounds including tannins, phenolic acids, anthocyanins, and fatty acids. These phytochemicals have potential to significantly impact on animal health and animal production. The goal of this work is to measure the effects of tannins in ground pine bark as a partial feed replacement on feed intake, dietary apparent digestibility, nitrogen balance, and mineral retention in meat goats. Results Eighteen Kiko cross goats (initial BW = 31.8 ± 1.49 kg) were randomly assigned to three treatment groups (n = 6). Dietary treatments were tested: control (0 % pine bark powder (PB) and 30 % wheat straw (WS)); 15 % PB and 15 % WS, and 30 % PB and 0 % WS. Although dry matter (DM) intake and digestibility were not affected (P > 0.10) by feeding PB, neutral detergent fiber (linear; P = 0.01), acid detergent fiber (linear; P = 0.001) and lignin digestibility (linear; P = 0.01) decreased, and crude protein (CP) digestibility tended to decrease (P = 0.09) as PB increased in the diet, apparent retention of Ca (P = 0.09), P (P = 0.03), Mg (P = 0.01), Mn (P = 0.01), Zn (P = 0.01) and Fe (P = 0.09) also increased linearly. Nitrogen intake and fecal N excretion were not affected (P > 0.05) by addition of PB in the diet, but N balance in the body was quadratically increased (P < 0.01) in the 15 % PB diet compared to other diets. This may be due to more rumen escape protein and less excreted N in the urine with the 15 % PB diet. The study showed that a moderate level of tannin-containing pine bark supplementation could improve gastrointestinal nitrogen balance with the aim of improving animal performance. Conclusion These results suggest that tannin-containing PB has negative impact on fiber, lignin, and protein digestibility, but positively impacted on N-balance.

Insect pollination reduces yield loss following heat stress in faba bean (Vicia faba L.)

Global food security, particularly crop fertilization and yield production, is threatened by heat waves that are projected to increase in frequency and magnitude with climate change. Effects of heat stress on the fertilization of insect-pollinated plants are not well understood, but experiments conducted primarily in self-pollinated crops, such as wheat, show that transfer of fertile pollen may recover yield following stress. We hypothesized that in the partially pollinator-dependent crop, faba bean (Vicia faba L.), insect pollination would elicit similar yield recovery following heat stress. We exposed potted faba bean plants to heat stress for 5 days during floral development and anthesis. Temperature treatments were representative of heat waves projected in the UK for the period 2021-2050 and onwards. Following temperature treatments, plants were distributed in flight cages and either pollinated by domesticated Bombus terrestris colonies or received no insect pollination. Yield loss due to heat stress at 30°C was greater in plants excluded from pollinators (15%) compared to those with bumblebee pollination (2.5%). Thus, the pollinator dependency of faba bean yield was 16% at control temperatures (18 to 26°C) and extreme stress (34°C), but was 53% following intermediate heat stress at 30°C. These findings provide the first evidence that the pollinator dependency of crops can be modified by heat stress, and suggest that insect pollination may become more important in crop production as the probability of heat waves increases.

Contribution of insect pollinators to crop yield and quality varies with agricultural intensification

Background: Up to 75% of crop species benefit at least to some degree from animal pollination for fruit or seed set and yield. However, basic information on the level of pollinator dependence and pollinator contribution to yield is lacking for many crops. Even less is known about how insect pollination affects crop quality. Given that habitat loss and agricultural intensification are known to decrease pollinator richness and abundance, there is a need to assess the consequences for different components of crop production. Methods: We used pollination exclusion on flowers or inflorescences on a whole plant basis to assess the contribution of insect pollination to crop yield and quality in four flowering crops (spring oilseed rape, field bean, strawberry, and buckwheat) located in four regions of Europe. For each crop, we recorded abundance and species richness of flower visiting insects in ten fields located along a gradient fromsimple to heterogeneous landscapes. Results: Insect pollination enhanced average crop yield between 18 and 71% depending on the crop. Yield quality was also enhanced in most crops. For instance, oilseed rape had higher oil and lower chlorophyll contents when adequately pollinated, the proportion of empty seeds decreased in buckwheat, and strawberries’ commercial grade improved; however, we did not find higher nitrogen content in open pollinated field beans. Complex landscapes had a higher overall species richness of wild pollinators across crops, but visitation rates were only higher in complex landscapes for some crops. On the contrary, the overall yield was consistently enhanced by higher visitation rates, but not by higher pollinator richness. Discussion. For the four crops in this study, there is clear benefit delivered by pollinators on yield quantity and/or quality, but it is not maximized under current agricultural intensification. Honeybees, the most abundant pollinator, might partially compensate the loss of wild pollinators in some areas, but our results suggest the need of landscape-scale actions to enhance wild pollinator populations.

Delaying senescence of wheat with fungicides has interacting effects with cultivar on grain sulphur concentration but not with sulphur yield or nitrogen: sulphur ratios

Winter wheat was grown in three field experiments, each repeated over two or three seasons, to investigate effects of extending flag leaf life by fungicide application on the concentration, kg ha(-1) and mg grain(-1) of nitrogen (N) and sulphur (S) as well as N:S ratio and sodium dodecyl sulphate (SDS) sedimentation volume. The experiments involved up to six cultivars and different application rates, timings and frequencies of azoxystrobin and epoxiconazole. For every day the duration to 37 % green flag leaf area (m) was extended, N yield was increased by 2.58 kg ha(-1), N per grain by 0.00957 mg, S yield by 0.186 kg ha(-1) and S per grain by 0.000718 mg. The N:S ratio decreased by 0.0135 per day. There was no evidence that these responses varied with cultivar. In contrast, the relationship between flag leaf life and N or S concentration interacted with cultivar. The N and S concentrations of Shamrock, the cultivar that suffered most from brown rust (Puccinia rccondita), increased with the extension of flag leaf life whereas the concentrations of N and S in Malacca, a cultivar more susceptible to Septoria tritici, decreased as flag leaf senescence was delayed. This was because the relationships between m and N and S yields were much better conserved over cultivars than those between m and thousand grain weight (TGW) and grain yield ha(-1). (c) 2004 Elsevier B.V. All rights reserved.

The effects of triazole and strobilurin fungicide programmes on nitrogen uptake, partitioning, remobilization and grain N accumulation in winter wheat cultivars

Field experiments were conducted over 3 years to assess the effect of a triazole fungicide programme, and additions of strobilurin fungicides to it, on nitrogen uptake, accumulation and partitioning in a range of winter wheat cultivars. Commensurate with delayed senescence, fungicide programmes, particularly when including strobilurins, improved grain yield through improvements in both crop biomass and harvest index, although the relationship with green area duration of the flag leaf (GFLAD) depended on year and in some cases, cultivar. In all years fungicide treatments significantly increased the amount of nitrogen in the above-ground biomass, the amount of nitrogen in the grain and the nitrogen harvest index. All these effects could be linearly related to the fungicide effect on GFLAD. These relationships occasionally interacted with cultivar but there was no evidence that fungicide mode of action affected the relationship between GFLAD and yield of nitrogen in the grain. Fungicide treatments significantly reduced the amount of soil mineral N at harvest and when severe disease had been controlled, the net remobilization of N from the vegetation to the grain after anthesis. Fungicide maintained the filling of grain with both dry matter and nitrogen. The proportionate accumulation of nitrogen in the grain was later than that of dry matter and this difference was greater when fungicide had been applied. Effects of fungicide on grain protein concentration and its relationship with GFLAD were inconsistent over year and cultivar. There were several instances where grain protein concentration was unaffected despite large (1(.)5 t/ha) increases in grain yield following fungicide use. Dilution of grain protein concentration following fungicide use, when it did occur, was small compared with what would be predicted by adoption of other yield increasing techniques such as the selection of high yielding cultivars (based on currently available cultivars) or by growing wheat in favourable climates.

Effect of prolonged intravenous glucose and essential amino acid infusion on nitrogen balance, muscle protein degradation and ubiquitin-conjugating enzyme gene expression in calves

Background: Intravenous infusions of glucose and amino acids increase both nitrogen balance and muscle accretion. We hypothesised that co-infusion of glucose ( to stimulate insulin) and essential amino acids (EAA) would act additively to improve nitrogen balance by decreasing muscle protein degradation in association with alterations in muscle expression of components of the ubiquitin-proteasome proteolytic pathway. Methods: We examined the effect of a 5 day intravenous infusions of saline, glucose, EAA and glucose + EAA, on urinary nitrogen excretion and muscle protein degradation. We carried out the study in 6 restrained calves since ruminants offer the advantage that muscle protein degradation can be assessed by excretion of 3 methyl-histidine and multiple muscle biopsies can be taken from the same animal. On the final day of infusion blood samples were taken for hormone and metabolite measurement and muscle biopsies for expression of ubiquitin, the 14-kDa E2 ubiquitin conjugating enzyme, and proteasome sub-units C2 and C8. Results: On day 5 of glucose infusion, plasma glucose, insulin and IGF-1 concentrations were increased while urea nitrogen excretion and myofibrillar protein degradation was decreased. Co-infusion of glucose + EAA prevented the loss of urinary nitrogen observed with EAA infusions alone and enhanced the increase in plasma IGF-1 concentration but there was no synergistic effect of glucose + EAA on the decrease in myofibrillar protein degradation. Muscle mRNA expression of the ubiquitin conjugating enzyme, 14-kDa E2 and proteasome sub-unit C2 were significantly decreased, after glucose but not amino acid infusions, and there was no further response to the combined infusions of glucose + EAA. Conclusion: Prolonged glucose infusion decreases myofibrillar protein degradation, prevents the excretion of infused EAA, and acts additively with EAA to increase plasma IGF-1 and improve net nitrogen balance. There was no evidence of synergistic effects between glucose + EAA infusion on muscle protein degradation or expression of components of the ubiquitin-proteasome proteolytic pathway.

Effects of two potential pest management components, intercropping and yellow sticky plastic sheet traps in two differentially resistant potato cultivars for the management of myzus persicae (Sulzer)

Polyculture is traditionally a low-input agricultural system and is important in many developing countries. Polycultures of interplanted crops often support fewer pests at lower densities than monoculture and tend to increase number of natural enemies. Also Yellow Sticky Plastic Sheet Traps have proved useful for trapping aphids. A field study was conducted to study the effectiveness of these potential pest management techniques along with the partially resistant (Cardinal) and susceptible (Desiree) potato cultivars, by using their different combinations for the management of Myzus persicae (Sulzer). Berseem, Trifolium alexandrinum (L.) (family: Leguminosae) was used for intercropping with potatoes. The different combinations (treatments) used in this study were: 1) Cardinal-berseem mixed cropping+yellow sticky plastic sheet traps 2) Cardinal-berseem mixed cropping 3) Cardinal+yellow sticky plastic sheet traps 4) Cardinal separately+berseem (as land area equivalents in relation to the mixed cropping treatments) 5) Cardinal (sole crop). Treatments 6-10 were the same treatments, but with Desiree as the potato cultivar. All these treatments were used to evaluate their effects as management techniques for M. persicae, their percent parasitism, percent emergence rate of the parasitoid, Aphidius matricariae Haliday and yield of Cardinal and Desiree. Mixed cropping of Cardinal and berseem together with the yellow sticky plastic sheet traps reduced aphids by over 90% compared with numbers on the sole Cardinal crop. This combination proved in this experiment the most effective for reducing the aphid populations as compared with all other treatments. Maximum percent parasitism i.e. 6.97 and 6.94% (almost double that in the other treatments) was recorded in the potato berseem mixed cropping, with and without traps respectively. In the same two treatments, yield was increased significantly as compared with all other treatments. However no significant effects of any of the variable was evident on the percent emergence of A. matricariae.

Effect of wheat dwarfing genes on nitrogen-use efficiency

Near isogenic lines (NILs) varying for alleles for reduced height (Rht) and photoperiod insensitivity (Ppd-D1a) in a cvar Mercia background (rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht8c+Ppd-D1a, Rht-D1c, Rht12) were compared at a field site in Berkshire, UK, but within different systems (‘organic’, O, in 2005/06, 2006/07 and 2007/08 growing seasons v. ‘conventional’, C, in 2005/06, 2006/07, 2007/08 and 2008/09). In 2007 and 2008, further NILs (rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht-B1b+Rht-D1b, Rht-D1b+Rht-B1c) in both Maris Huntsman and Maris Widgeon backgrounds were added. The contrasting systems allowed NILs to be tested in diverse rotational and agronomic, but commercially relevant, contexts, particularly with regard to the assumed temporal distribution of nitrogen availability, and competition from weeds. For grain, nitrogen-use efficiency (NUE; grain dry matter (DM) yield/available N; where available N=fertilizer N+soil mineral N), recovery of N in the grain (grain N yield/available N), N utilization efficiency to produce grain (NUtEg; grain DM yield/above-ground crop N yield), N harvest index (grain N yield/above-ground crop N yield) and dry matter harvest index (DMHI; grain DM yield/above-ground crop DM yield) all peaked at final crop heights of 800–950 mm. Maximum NUE occurred at greater crop heights in the organic system than in the conventional system, such that even adding just a semi-dwarfing allele (Rht-D1b) to the shortest background, Mercia, reduced NUE in the organic system. The mechanism of dwarfing (gibberellin sensitive or insensitive) made little difference to the relationship between NUE and its components with crop height. For above-ground biomass: dwarfing alleles had a greater effect on DM accumulation compared with N accumulation such that all dwarfing alleles could reduce nitrogen utilization efficiency (NUtE; crop DM yield/crop N yield). This was particularly evident at anthesis in the conventional system when there was no significant penalty for severe dwarfism for N accumulation, despite a 3-tonne (t)/ha reduction in biomass compared to the tallest lines. Differences between genotypes for recovery of N in the grain were thus mostly a function of net N uptake after anthesis rather than of remobilized N. This effect was compounded as dwarfing, except when coupled with Ppd-D1a, was associated with delayed anthesis. In the organic experiments there was greater reliance on N accumulated before anthesis, and genotype effects on NUE were confounded with effects on N accumulated by weeds, which was negatively associated with crop height. Optimum height for maximizing wheat NUE and its components, as manipulated by Rht alleles, thus depend on growing system, and crop utilization (i.e. biomass or grain production).

Contrasting effects of dwarfing alleles and nitrogen availability on mineral concentrations in wheat grain

Background and aim Concentrations of essential minerals in plant foods may have declined in modern high-yielding cultivars grown with large applications of nitrogen fertilizer (N). We investigated the effect of dwarfing alleles and N rate on mineral concentrations in wheat. Methods Gibberellin (GA)-insensitive reduced height (Rht) alleles were compared in near isogenic wheat lines. Two field experiments comprised factorial combinations of wheat variety backgrounds, alleles at the Rht-B1 locus (rht-B1a, Rht-B1b, Rht-B1c), and different N rates. A glasshouse experiment also included Rht-D1b and Rht-B1b+D1b in one background. Results In the field, depending on season, Rht-B1b increased crop biomass, dry matter (DM) harvest index, grain yield, and the economically-optimal N rate (Nopt). Rht-B1b did not increase uptake of Cu, Fe, Mg or Zn so these minerals were diluted in grain. Nitrogen increased DM yield and mineral uptake so grain concentrations were increased (Fe in both seasons; Cu, Mg and Zn in one season). Rht-B1b reduced mineral concentrations at Nopt in the most N responsive season. In the glasshouse experiment, grain yield was reduced, and mineral concentrations increased, with Rht allele addition. Conclusion Effects of Rht alleles on Fe, Zn, Cu and Mg concentrations in wheat grain are mostly due to their effects on DM, rather than of GA-insensitivity on Nopt or mineral uptake. Increased N requirement in semi-dwarf varieties partly offsets this dilution effect.